Demo Vignettes
Welcome to this collection of vignettes that demonstrate the various capabilities and uses of epymorph.
Single-node usage
1. Intro to Epymorph
Creating a single-node SIR model and showcasing the basic simulation and visualization capabilities of epymorph.
2. Birth and Death
Creating an SIR model with host demography, to visualize damped oscillations.
3. Hospitalization
Creating an SIRH model (with hospitalization), showcasing forking in the IPM specification.
4. Time-varying Transmission Rate
Creating an SIRS model with seasonal forcing, demonstrating epymorph’s method of specifying function-based parameter values.
5. Parameter Estimation with Particle Filtering
Using simulated and real hospitalization data to estimate time-varying transmission rate with epymorph’s built-in particle filter methods.
Multi-node usage
1. Intro to Movement Models
Creating multi-node simulations, demonstrating movement models of various complexity, and introduction to the choropleth mapping functionality.
2. Age-stratified, multi-node SIRH model with multiple movement models
Creating a multi-strate RUME, exploring how to add different movement models per strata.
3. Location- and Time-varying Parameter Estimation with Particle Filtering
Using real hospitalization data to estimate State-specific and time-varying transmission rates with epymorph’s particle filter with localization.
Feel free to explore each vignette in order or jump to the one that interests you the most.